Sure, all of the actresses from the series nominated in the guest actress category — Aduba, Cox, and Natasha Lyonne — are all on screen just as much as their supporting actress counterparts, but they're still considered guest stars in the series because of their contracts. So, since Aduba wasn't upgraded to a series regular until just before season 2, and Orange Is the New Black was only eligible to submit their nominations this year for the first season, Aduba was still considered a guest star for the episodes that the voters are considering.

The reason that Mulgrew was able to be nominated as a supporting actress is the same: Contractually, she was a series regular during the first season.

So, question answered. Now, can we just enjoy the fact that this show got so much recognition?